BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365362.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 603,486,254 number of mapped reads = 577,411,013 (95.68%) number of supplementary alignments = 68,817,492 (11.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 288,645,628 number of mapped paired reads (second in pair) = 288,765,385 number of mapped paired reads (both in pair) = 573,028,512 number of mapped paired reads (singletons) = 4,382,501 number of mapped bases = 76,048,744,630 bp number of sequenced bases = 75,907,610,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,070,023 duplication rate = 34.92% >>>>>>> Insert size mean insert size = 186,228.1723 std insert size = 3,509,957.1377 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.5233 >>>>>>> ACTG content number of A's = 20,891,799,800 bp (27.52%) number of C's = 17,113,783,750 bp (22.55%) number of T's = 20,447,603,262 bp (26.94%) number of G's = 17,454,135,274 bp (22.99%) number of N's = 288,526 bp (0%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0218 number of mismatches = 1,459,331,875 number of insertions = 40,419,358 mapped reads with insertion percentage = 6.14% number of deletions = 33,335,127 mapped reads with deletion percentage = 5.16% homopolymer indels = 35.1% >>>>>>> Coverage mean coverageData = 24.566X std coverageData = 1,220.6917X There is a 69.7% of reference with a coverageData >= 1X There is a 65.63% of reference with a coverageData >= 2X There is a 58.01% of reference with a coverageData >= 3X There is a 54.69% of reference with a coverageData >= 4X There is a 50.01% of reference with a coverageData >= 5X There is a 47.2% of reference with a coverageData >= 6X There is a 43.88% of reference with a coverageData >= 7X There is a 41.5% of reference with a coverageData >= 8X There is a 38.96% of reference with a coverageData >= 9X There is a 36.94% of reference with a coverageData >= 10X There is a 34.89% of reference with a coverageData >= 11X There is a 33.17% of reference with a coverageData >= 12X There is a 31.47% of reference with a coverageData >= 13X There is a 29.98% of reference with a coverageData >= 14X There is a 28.54% of reference with a coverageData >= 15X There is a 27.24% of reference with a coverageData >= 16X There is a 26% of reference with a coverageData >= 17X There is a 24.87% of reference with a coverageData >= 18X There is a 23.79% of reference with a coverageData >= 19X There is a 22.8% of reference with a coverageData >= 20X There is a 21.85% of reference with a coverageData >= 21X There is a 20.97% of reference with a coverageData >= 22X There is a 20.13% of reference with a coverageData >= 23X There is a 19.34% of reference with a coverageData >= 24X There is a 18.59% of reference with a coverageData >= 25X There is a 17.88% of reference with a coverageData >= 26X There is a 17.21% of reference with a coverageData >= 27X There is a 16.58% of reference with a coverageData >= 28X There is a 15.97% of reference with a coverageData >= 29X There is a 15.4% of reference with a coverageData >= 30X There is a 14.86% of reference with a coverageData >= 31X There is a 14.34% of reference with a coverageData >= 32X There is a 13.85% of reference with a coverageData >= 33X There is a 13.38% of reference with a coverageData >= 34X There is a 12.93% of reference with a coverageData >= 35X There is a 12.5% of reference with a coverageData >= 36X There is a 12.09% of reference with a coverageData >= 37X There is a 11.7% of reference with a coverageData >= 38X There is a 11.33% of reference with a coverageData >= 39X There is a 10.97% of reference with a coverageData >= 40X There is a 10.63% of reference with a coverageData >= 41X There is a 10.3% of reference with a coverageData >= 42X There is a 9.99% of reference with a coverageData >= 43X There is a 9.69% of reference with a coverageData >= 44X There is a 9.4% of reference with a coverageData >= 45X There is a 9.12% of reference with a coverageData >= 46X There is a 8.85% of reference with a coverageData >= 47X There is a 8.59% of reference with a coverageData >= 48X There is a 8.35% of reference with a coverageData >= 49X There is a 8.11% of reference with a coverageData >= 50X There is a 7.88% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5054070032 20.277060942608443 552.4941984582053 chr2 243199373 5528866435 22.73388441260496 743.7000022289961 chr3 198022430 3184220221 16.080098709019982 237.2979338466707 chr4 191154276 5646581740 29.539395393906858 2495.819105151672 chr5 180915260 2898074763 16.01896248553052 100.39093708758467 chr6 171115067 2839437373 16.593730889869562 411.9157726085496 chr7 159138663 3390291331 21.304007882735572 240.21936872115378 chr8 146364022 2672057927 18.256248294406667 189.17159560088746 chr9 141213431 2597555643 18.394536727883906 518.3252744670089 chr10 135534747 6371623159 47.0109938597517 2863.5208607156037 chr11 135006516 2946548642 21.825232805800276 171.94990800255547 chr12 133851895 2570191126 19.201753744315685 96.25370466932095 chr13 115169878 1220240544 10.59513620392999 30.470271168528022 chr14 107349540 1624511308 15.132913545786968 88.2734409289255 chr15 102531392 1541126959 15.030781587360094 44.684316886396246 chr16 90354753 4688063464 51.88507863000854 1580.3312687722412 chr17 81195210 2576075531 31.726939692624725 928.696942928653 chr18 78077248 2512765653 32.1830714755725 2927.7417609520185 chr19 59128983 2271620589 38.418056150230086 448.22772801387106 chr20 63025520 1695990283 26.909580166891125 954.6196470134652 chr21 48129895 1716325921 35.66028808082793 1393.3115588637954 chr22 51304566 1152812496 22.469978520040495 110.49205162019813 chrMT 16571 30134326 1818.49773701044 1197.2213375262024 chrX 155270560 1736409727 11.183122718176582 217.3464034640133 chrY 59373566 7583149437 127.7192856666214 3812.0358307741